wwPDB validation reports are now provided in PDBx/mmCIF format for all
new depositions in OneDep. This change makes validation data more
interoperable with the PDB archival format. Data are more logically and
better organized in the PDBx/mmCIF reports, and therefore more
“database-friendly” than the report in XML format. PDBx/mmCIF-format
validation reports for newly released and modified entries will be
distributed through the PDB
<https://ftp.wwpdb.org/pub/pdb/validation_reports/> and EMDB
<https://ftp.wwpdb.org/pub/emdb/validation_reports/> Core Archives.
The new PDBx/mmCIF reports are easier to interpret. They contain a
high-level summary and offer easier access to residue-level information.
Data are provided at multiple levels: entity, chain-specific, and even
at the individual residues. For example, it is more straightforward to
obtain the total number of clashes. The corresponding validation
dictionary is available at
mmcif.wwpdb.org/dictionaries/mmcif_pdbx_vrpt.dic/Index
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_vrpt.dic/Index/>.
Examples of PDBx/mmCIF validation reports for X-ray, 3DEM, and NMR are
publicly available at GitHub
<https://github.com/wwPDB/validation-mmcif-examples>.
PDBx/mmCIF validation reports will be provided for the full PDB and EMDB
archives once archival validation recalculation is performed.
wwPDB strongly recommends all PDB users and software developers adopt
this format for future applications.
--
Regards,
Jasmine
===========================================================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
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